I would guess the fans that don't like AFL would constitute a small minority of soccer fans in general. To say that they can ruin their following because of their dislike of AFL is a weak argument.AFL is the stronger code in Australia, I'd say that fans are aware of the threat that soccer has but certainly don't have an inferiority complex. Some will say things like "soccer is boring", "why do those fools bring flares", "if they need to sing and chant then obviously the game isn't interesting", etc... However, there are is a fair section of AFL fans who like soccer and there are also those who will occassionally watch it (i.e. World Cup, important qualifiers, etc...) and respect that it is a good sport.
However, if you have a look over at the Victory forums, for example, some of the comments there are ridiculous. While there are a lot of AFL fans who now follow the A-League, for those that don't follow the AFL, they think it is the devils sport and that anyone or anything that is remotely linked to AFL is pure evil. They harp on about averaging 30,000 fans, well if they continue to alienate the AFL fans within, then it will go back to 4,000 fans like the NSL.